I should start by saying as clearly as I can that I love antibiotics. Recently I had dinner with a paediatrician friend, and she told me the story of the day's sickest child.

Before she sent the child to the emergency room in an ambulance, she told me, she gave her 50 milligrams per kilogram of a powerful antibiotic. "You probably saved her life," I said, and my friend nodded; it was possible.

Antibiotics represent a huge gift in the struggle against infant and child mortality, a triumph (or actually, many triumphs) of human ingenuity and science over disease and death, since the antibiotic era began back in the fourth and fifth decades of the 20th century.

But new research is looking at questions about the complex effects of antibiotics — on bacteria, on individual children and on populations — building on a greatly increased awareness of how powerful antibiotics can be and how important it is to use them judiciously.

Over the past 15 years or so, spurred by new realisations — and new fears — about the risks of breeding resistant strains of bacteria, paediatricians in the United States have cut back dramatically on prescribing antibiotics in situations where they may not be necessary.

And parents have become less likely to demand them. "It's actually been a remarkable change in practice from the mid-90s on," said Dr. Jonathan Finkelstein, a paediatrician at Boston Children's Hospital who studies antibiotic use and antibiotic resistance, "and we did that by physicians and patients recognising that antibiotics are quite effective, quite safe, but there's no such thing as a free lunch, and as with any other medical decision, we have to weigh the risks and benefits of every treatment".

No antibiotics are needed for those upper respiratory infections — colds, coughs, runny noses — that are caused by viruses. There has been a lot of discussion of whether ear infections should always be treated with antibiotics or whether in some situations (older child, less ill) 'watchful waiting' may be appropriate — but it's also true that many of us have become reluctant to diagnose ear infections in borderline cases.

In a study that Finkelstein and his colleagues published this year, looking at antibiotic use in children in Massachusetts, the rate at which antibiotics were dispensed to the youngest group (3 to 24 months) had decreased 24 per cent by 2008-09 from 2000-01.

And that drop was largely driven by a declining rate of diagnosis of ear infections. We always knew there were immediate risks to antibiotics. Children could have allergic reactions.

They could get diarrhoea. Babies could get unpleasant yeast infections — severe diaper rash, thrush in the mouth. But still, the thinking back when I trained in the '80s was that after the antibiotics, the body would return to normal.

"When antibiotics were developed, they were miraculous for all the reasons that you know," said Martin J. Blaser, the chairman of medicine at New York University School of Medicine.

"With few exceptions, there was almost no long-term toxicity that was identifiable, and so everybody thought that if you took an antibiotic it could produce some immediate upset — it could produce a rash, loose bowels — and then everything would return to normal, bounce back to normal. But in fact there was no real exploration of that.

Blaser has devoted himself to a study of what is called the microbiome, the bacterial population that lives on us and in us, and the effects of perturbing that population by antibiotic use. He and other researchers are asking whether alterations in the microbiome may be linked to many different patterns of health, growth and disease. It's an area of investigation that is still new but changing quickly.

And there is the question of a connection between antibiotics and obesity, which arises in part, Blaser said, because of the practice of feeding antibiotics to livestock to increase weight — although the mechanism by which that works is not understood.

The influence of early antibiotics on the lungs has also been examined; several studies have looked at possible associations between antibiotics in pregnancy, infancy and childhood and the later development of asthma — a review last year concluded the additional risk from antibiotics was slight.

Children who need antibiotics should get them. But new studies challenge us to think about the effects of antibiotics on the bacterial populations that accompany us through life and to treat the great gift of antibiotics with deeper understanding and respect.